It's no big secret. Sometimes I drink a lot, hug the toilet, vomit so violently that my body contorts into weird possitions that are not usual for some muscles and they get hurt. Mostly in my neck and shoulder. It's a sign that I had a "good time".
A little shoulder pain shouldn't be enough to stop sex. That's what the girl-on-top position is for. Or just bend her over something and fuck her from behind standing up.